DGRPool

GWAS results were computed on dm3 genome.

If you want to make an independent analysis with DGRP2 or PLINK2, you can find here prepared input files for this phenotype: DGRP2 results PLINK2 results

Full results

Phenotype distribution and association to known covariates

Shapiro-Wilk test of normality (p-value=4.093e^-27)
Null Hypothesis is rejected (p<=0.05).
Interpretation: NOT NORMAL distribution of this phenotype

We tested for association of this phenotype with 6 known covariates Huang et al., 2014 using both ANOVA and Kruskal-Wallis association tests.

ANOVA test
No significant result.

Kruskal-Wallis test

Covariate	χ²	p-value	Significance
wolba	3.1463	0.0761
In_3R_P	5.8823	0.0528

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

12545 significant hits at p-value < 0.001. The 1000 top results are displayed in the table below.

We performed a gene enrichment calculation (Fisher's exact test) of all GWAS-associated genes at p < 0.001. Genesets were taken from two database: the Gene Ontology (GO) and the FlyBase phenotypes. GO enrichment FlyBase phenotype enrichment

Variant impact HIGH MODERATE LOW MODIFIER

Show entries

Search:

Chromosome	Position	ID	Reference	Variant	p-value	FDR_BH	Transcript annotation	Binding site annotation
X	8837232	X_8837232_SNP [dm3] X_8943199_SNP [dm6]	T	C	1.734e^-18	3.252e^-12	INTRON rdgA
2R	8193131	2R_8193131_SNP [dm3] 2R_12305626_SNP [dm6]	C	A	2.913e^-17	2.732e^-11	SYNONYMOUS_CODING SIP2 UPSTREAM CG17739	TF binding site mE1_TFBS_inv
3R	3820087	3R_3820087_SNP [dm3] 3R_7994365_SNP [dm6]	G	T	5.014e^-17	3.135e^-11	INTRON CG2781
2R	8242479	2R_8242479_SNP [dm3] 2R_12354974_SNP [dm6]	C	T	7.290e^-17	3.419e^-11	SYNONYMOUS_CODING CG30047 UPSTREAM CG30049	TF binding site mE1_TFBS_sens
X	9283746	X_9283746_SNP [dm3] X_9389713_SNP [dm6]	G	A	9.997e^-17	3.750e^-11	INTRON mgl
3L	4092421	3L_4092421_SNP [dm3] 3L_4092421_SNP [dm6]	T	C	1.464e^-16	4.577e^-11	UTR_3_PRIME CG14989 UPSTREAM CG14990	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
2R	8242496	2R_8242496_SNP [dm3] 2R_12354991_SNP [dm6]	C	T	1.745e^-16	4.675e^-11	SYNONYMOUS_CODING CG30047 UPSTREAM CG30049	TF binding site mE1_TFBS_sens
3L	13072190	3L_13072190_SNP [dm3] 3L_13079090_SNP [dm6]	A	T	3.209e^-16	7.525e^-11	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_cad mE1_TFBS_HSA
3L	15633584	3L_15633584_SNP [dm3] 3L_15640484_SNP [dm6]	A	G	1.462e^-15	3.046e^-10	INTRON comm3	TF binding site mE1_TFBS_hkb
3L	13254694	3L_13254694_SNP [dm3] 3L_13261594_SNP [dm6]	G	T	1.915e^-15	3.592e^-10	INTRON caps
3L	12401626	3L_12401626_SNP [dm3] 3L_12408526_SNP [dm6]	T	G	3.106e^-15	5.297e^-10	UTR_5_PRIME CG32103 INTRON CG32103	TF binding site mE1_TFBS_cad
X	8837229	X_8837229_DEL [dm3] X_8943196_DEL [dm6]	CC	A	3.580e^-15	5.596e^-10	INTRON rdgA
3R	11839112	3R_11839112_SNP [dm3] 3R_16013390_SNP [dm6]	G	A	1.112e^-14	1.533e^-9	INTRON GATAe	TF binding site BDTNP1_TFBS_da mE1_TFBS_HSA
X	8512828	X_8512828_SNP [dm3] X_8618795_SNP [dm6]	A	G	1.144e^-14	1.533e^-9	INTERGENIC	regulatory region REDfly_CRMs
2R	10700517	2R_10700517_SNP [dm3] 2R_14813012_SNP [dm6]	T	A	1.238e^-14	1.548e^-9	INTERGENIC	regulatory region REDfly_CRMs
3R	23545248	3R_23545248_SNP [dm3] 3R_27719526_SNP [dm6]	C	A	9.728e^-14	1.140e^-8	INTERGENIC	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
3L	13238037	3L_13238037_SNP [dm3] 3L_13244937_SNP [dm6]	A	T	1.252e^-13	1.381e^-8	INTRON caps	TF binding site BDTNP1_TFBS_dl
X	10200344	X_10200344_SNP [dm3] X_10306311_SNP [dm6]	C	T	1.890e^-13	1.969e^-8	INTRON alpha-Man-I
3L	13254540	3L_13254540_SNP [dm3] 3L_13261440_SNP [dm6]	A	T	2.836e^-13	2.723e^-8	INTRON caps
3R	13298125	3R_13298125_SNP [dm3] 3R_17472403_SNP [dm6]	A	T	2.904e^-13	2.723e^-8	INTERGENIC
3R	7194630	3R_7194630_INS [dm3] 3R_11368908_INS [dm6]	A	AAAGTACAA	5.307e^-13	4.740e^-8	INTRON pros	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_inv
3L	7720298	3L_7720298_DEL [dm3] 3L_7727198_DEL [dm6]	CGCTGAAAAAGT...	C	8.292e^-13	7.069e^-8	UPSTREAM CG7457 DOWNSTREAM CG8492 INTRON CG32373	TF binding site mE1_TFBS_HSA
3R	23509215	3R_23509215_SNP [dm3] 3R_27683493_SNP [dm6]	A	T	1.695e^-12	1.382e^-7	INTERGENIC	TF binding site mE1_TFBS_chinmo
3R	10343265	3R_10343265_SNP [dm3] 3R_14517543_SNP [dm6]	C	G	2.319e^-12	1.812e^-7	DOWNSTREAM CG34273 INTRON Pde6
3R	7194296	3R_7194296_SNP [dm3] 3R_11368574_SNP [dm6]	T	A	2.927e^-12	2.196e^-7	INTRON pros	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_inv mE1_TFBS_sens
X	15198172	X_15198172_SNP [dm3] X_15304139_SNP [dm6]	G	A	6.048e^-12	4.363e^-7	INTRON gce
3R	10442861	3R_10442861_SNP [dm3] 3R_14617139_SNP [dm6]	A	G	8.887e^-12	6.174e^-7	INTRON CG14853	TF binding site mE1_TFBS_cad
3L	3923160	3L_3923160_SNP [dm3] 3L_3923160_SNP [dm6]	C	G	9.336e^-12	6.254e^-7	INTRON Eip63F-1
3R	3827036	3R_3827036_SNP [dm3] 3R_8001314_SNP [dm6]	G	T	1.266e^-11	8.190e^-7	UPSTREAM CG2698 & 1 other DOWNSTREAM CG14463 INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_z mE1_TFBS_HSA mE1_TFBS_jumu
3R	7527076	3R_7527076_SNP [dm3] 3R_11701354_SNP [dm6]	G	A	1.322e^-11	8.264e^-7	SYNONYMOUS_CODING CG14718	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
3R	5151733	3R_5151733_SNP [dm3] 3R_9326011_SNP [dm6]	T	A	1.380e^-11	8.352e^-7	INTRON CG8861
3L	13254716	3L_13254716_DEL [dm3] 3L_13261616_DEL [dm6]	CAT	C	1.839e^-11	1.071e^-6	INTRON caps
2R	8244303	2R_8244303_SNP [dm3] 2R_12356798_SNP [dm6]	G	A	1.884e^-11	1.071e^-6	SYNONYMOUS_CODING CG30049	TF binding site mE1_TFBS_HSA
3L	16131567	3L_16131567_SNP [dm3] 3L_16138467_SNP [dm6]	C	A	2.417e^-11	1.333e^-6	UTR_3_PRIME CG5151 UPSTREAM CG5157
2R	9581722	2R_9581722_SNP [dm3] 2R_13694217_SNP [dm6]	G	C	2.576e^-11	1.380e^-6	UPSTREAM CG6220 INTRON fas	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
3L	14270282	3L_14270282_SNP [dm3] 3L_14277182_SNP [dm6]	T	C	3.103e^-11	1.603e^-6	INTRON fz	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
2R	14219529	2R_14219529_SNP [dm3] 2R_18332024_SNP [dm6]	G	C	3.162e^-11	1.603e^-6	INTRON sbb	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_inv
X	13140884	X_13140884_DEL [dm3] X_13246851_DEL [dm6]	AA	A	3.631e^-11	1.771e^-6	INTRON mew	TF binding site BDTNP1_TFBS_da mE1_TFBS_HSA mE1_TFBS_inv
3R	25466016	3R_25466016_SNP [dm3] 3R_29640294_SNP [dm6]	G	A	3.682e^-11	1.771e^-6	SYNONYMOUS_CODING Dop1R2
3L	16561580	3L_16561580_SNP [dm3] 3L_16568480_SNP [dm6]	A	T	3.879e^-11	1.819e^-6	INTRON Mipp1
3R	26043835	3R_26043835_SNP [dm3] 3R_30218113_SNP [dm6]	C	T	4.152e^-11	1.900e^-6	INTERGENIC
X	8837224	X_8837224_SNP [dm3] X_8943191_SNP [dm6]	G	A	4.501e^-11	1.963e^-6	INTRON rdgA
X	8837225	X_8837225_SNP [dm3] X_8943192_SNP [dm6]	T	A	4.501e^-11	1.963e^-6	INTRON rdgA
X	8837218	X_8837218_DEL [dm3] X_8943185_DEL [dm6]	AAACA	A	5.174e^-11	2.206e^-6	INTRON rdgA
2L	19985708	2L_19985708_SNP [dm3] 2L_19985708_SNP [dm6]	A	T	5.481e^-11	2.285e^-6	INTRON CG43861	TF binding site mE1_TFBS_inv
X	14601920	X_14601920_SNP [dm3] X_14707887_SNP [dm6]	A	G	8.325e^-11	3.395e^-6	INTRON NetB
2R	11544440	2R_11544440_SNP [dm3] 2R_15656935_SNP [dm6]	G	A	1.057e^-10	4.217e^-6	UTR_3_PRIME CG42524 UPSTREAM mir-278 DOWNSTREAM fus	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
2R	14667099	2R_14667099_SNP [dm3] 2R_18779594_SNP [dm6]	A	G	1.142e^-10	4.464e^-6	INTERGENIC
3L	20508654	3L_20508654_SNP [dm3] 3L_20515554_SNP [dm6]	G	T	1.183e^-10	4.530e^-6	SYNONYMOUS_CODING CG5059	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad
3L	2835206	3L_2835206_SNP [dm3] 3L_2835206_SNP [dm6]	T	A	1.342e^-10	5.036e^-6	INTRON CG43444
3L	22708230	3L_22708230_SNP [dm3] 3L_22715130_SNP [dm6]	G	A	1.390e^-10	5.063e^-6	INTRON ArfGAP3
3L	16618907	3L_16618907_SNP [dm3] 3L_16625807_SNP [dm6]	C	T	1.404e^-10	5.063e^-6	INTRON Abl	TF binding site BDTNP1_TFBS_dl
3L	16135763	3L_16135763_SNP [dm3] 3L_16142663_SNP [dm6]	C	T	1.532e^-10	5.420e^-6	NON_SYNONYMOUS_CODING CG32152 UTR_5_PRIME CG5151 INTRON CG5151
X	15198500	X_15198500_SNP [dm3] X_15304467_SNP [dm6]	A	T	1.579e^-10	5.484e^-6	INTRON gce
3R	6137862	3R_6137862_SNP [dm3] 3R_10312140_SNP [dm6]	T	C	1.622e^-10	5.489e^-6	UTR_3_PRIME Bruce UPSTREAM CG6293	TF binding site mE1_TFBS_cad
3R	26828557	3R_26828557_SNP [dm3] 3R_31002835_SNP [dm6]	T	G	1.639e^-10	5.489e^-6	INTRON 5-HT7
3R	26002844	3R_26002844_SNP [dm3] 3R_30177122_SNP [dm6]	G	A	1.707e^-10	5.617e^-6	UPSTREAM CG15530 INTRON CG1983
3L	14115499	3L_14115499_SNP [dm3] 3L_14122399_SNP [dm6]	T	G	1.780e^-10	5.731e^-6	INTRON Sox21b	TF binding site BDTNP1_TFBS_dl
3R	25466632	3R_25466632_SNP [dm3] 3R_29640910_SNP [dm6]	A	G	1.803e^-10	5.731e^-6	SYNONYMOUS_CODING Dop1R2	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
2R	14667105	2R_14667105_SNP [dm3] 2R_18779600_SNP [dm6]	A	T	1.922e^-10	6.007e^-6	INTERGENIC
3R	10440157	3R_10440157_SNP [dm3] 3R_14614435_SNP [dm6]	C	T	2.003e^-10	6.158e^-6	INTRON CG14853
3L	4184517	3L_4184517_SNP [dm3] 3L_4184517_SNP [dm6]	T	G	2.088e^-10	6.247e^-6	SYNONYMOUS_CODING Teh3 INTRON CG18675 & 1 other	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
3R	25988915	3R_25988915_SNP [dm3] 3R_30163193_SNP [dm6]	C	T	2.098e^-10	6.247e^-6	INTERGENIC
3R	25563014	3R_25563014_SNP [dm3] 3R_29737292_SNP [dm6]	C	T	2.382e^-10	6.981e^-6	SYNONYMOUS_CODING CG7598 UPSTREAM CG7601 & 1 other	TF binding site mE1_TFBS_sens mE1_TFBS_Ubx
3L	20494860	3L_20494860_SNP [dm3] 3L_20501760_SNP [dm6]	G	A	2.448e^-10	7.004e^-6	DOWNSTREAM CG18281 INTRON CG32425	transposable element FlyBase
3L	2590625	3L_2590625_SNP [dm3] 3L_2590625_SNP [dm6]	A	C	2.533e^-10	7.004e^-6	UTR_5_PRIME dos INTRON dos	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_Kr mE1_TFBS_Stat92E
2R	8222446	2R_8222446_DEL [dm3] 2R_12334941_DEL [dm6]	CTTTTAAAAAATTAAAAAGA...	C	2.538e^-10	7.004e^-6	UPSTREAM tRNA:CR30249 & 2 others DOWNSTREAM tRNA:CR30251 INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_HSA
2R	14993373	2R_14993373_SNP [dm3] 2R_19105868_SNP [dm6]	A	T	2.557e^-10	7.004e^-6	INTRON 5-HT1A
3L	16138978	3L_16138978_SNP [dm3] 3L_16145878_SNP [dm6]	T	G	2.586e^-10	7.004e^-6	INTRON CG5151	TF binding site mE1_TFBS_Trl
3R	25467034	3R_25467034_SNP [dm3] 3R_29641312_SNP [dm6]	G	A	2.633e^-10	7.004e^-6	SYNONYMOUS_CODING Dop1R2	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
2R	8183687	2R_8183687_SNP [dm3] 2R_12296182_SNP [dm6]	G	C	2.651e^-10	7.004e^-6	DOWNSTREAM CR45271 INTRON CG42700
3R	7163818	3R_7163818_SNP [dm3] 3R_11338096_SNP [dm6]	T	A	2.751e^-10	7.114e^-6	INTRON pros
3R	6842426	3R_6842426_SNP [dm3] 3R_11016704_SNP [dm6]	T	C	2.769e^-10	7.114e^-6	INTRON CG34114
3L	7716497	3L_7716497_SNP [dm3] 3L_7723397_SNP [dm6]	C	T	2.870e^-10	7.196e^-6	SYNONYMOUS_CODING CG7457 INTRON CG32373
2L	16485055	2L_16485055_SNP [dm3] 2L_16485055_SNP [dm6]	G	A	2.877e^-10	7.196e^-6	INTRON dac	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_hb
3R	25465938	3R_25465938_SNP [dm3] 3R_29640216_SNP [dm6]	G	A	2.969e^-10	7.327e^-6	INTRON Dop1R2
3L	17360676	3L_17360676_SNP [dm3] 3L_17367576_SNP [dm6]	T	G	3.359e^-10	8.183e^-6	DOWNSTREAM Cad74A & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_HSA
3R	10978581	3R_10978581_SNP [dm3] 3R_15152859_SNP [dm6]	C	A	3.432e^-10	8.228e^-6	INTRON Gyc88E
3L	16131973	3L_16131973_SNP [dm3] 3L_16138873_SNP [dm6]	C	T	3.465e^-10	8.228e^-6	UTR_3_PRIME CG5151 UPSTREAM CG5157 DOWNSTREAM CG5151 & 1 other
X	7863423	X_7863423_SNP [dm3] X_7969390_SNP [dm6]	T	G	3.565e^-10	8.359e^-6	UPSTREAM sn INTRON sn	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_D mE1_TFBS_GATAe mE1_TFBS_h mE1_TFBS_HSA mE1_TFBS_run mE1_TFBS_sens mE1_TFBS_Trl
3R	26116556	3R_26116556_SNP [dm3] 3R_30290834_SNP [dm6]	C	T	3.927e^-10	9.093e^-6	INTRON hdc
3L	10445864	3L_10445864_SNP [dm3] 3L_10452764_SNP [dm6]	A	C	4.043e^-10	9.248e^-6	INTERGENIC
X	10045050	X_10045050_SNP [dm3] X_10151017_SNP [dm6]	G	A	4.212e^-10	9.518e^-6	INTRON CR44894
3R	25563247	3R_25563247_SNP [dm3] 3R_29737525_SNP [dm6]	T	C	4.369e^-10	9.642e^-6	UPSTREAM CG7601 & 1 other INTRON CG7598	TF binding site BDTNP1_TFBS_dl mE1_TFBS_sens
3R	25563253	3R_25563253_SNP [dm3] 3R_29737531_SNP [dm6]	T	G	4.369e^-10	9.642e^-6	UPSTREAM CG7601 & 1 other INTRON CG7598	TF binding site BDTNP1_TFBS_dl mE1_TFBS_sens
3R	6842621	3R_6842621_SNP [dm3] 3R_11016899_SNP [dm6]	A	T	4.745e^-10	1.035e^-5	INTRON CG34114
3L	12723974	3L_12723974_SNP [dm3] 3L_12730874_SNP [dm6]	G	A	4.915e^-10	1.060e^-5	INTERGENIC
3L	12985319	3L_12985319_SNP [dm3] 3L_12992219_SNP [dm6]	A	T	5.238e^-10	1.113e^-5	INTERGENIC
3R	10461907	3R_10461907_SNP [dm3] 3R_14636185_SNP [dm6]	C	T	5.280e^-10	1.113e^-5	SYNONYMOUS_CODING Cad88C INTRON CG7886	TF binding site mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
3R	10251690	3R_10251690_SNP [dm3] 3R_14425968_SNP [dm6]	G	A	5.708e^-10	1.190e^-5	INTRON cv-c
3R	10251743	3R_10251743_SNP [dm3] 3R_14426021_SNP [dm6]	C	A	5.890e^-10	1.214e^-5	INTRON cv-c
2L	3679010	2L_3679010_SNP [dm3] 2L_3679010_SNP [dm6]	T	C	5.969e^-10	1.217e^-5	INTRON CG34340
3R	25602927	3R_25602927_SNP [dm3] 3R_29777205_SNP [dm6]	C	T	6.127e^-10	1.236e^-5	INTRON kay
3L	7728151	3L_7728151_SNP [dm3] 3L_7735051_SNP [dm6]	G	T	6.246e^-10	1.245e^-5	INTRON CG32373 & 1 other
3L	17808834	3L_17808834_SNP [dm3] 3L_17815734_SNP [dm6]	C	T	6.310e^-10	1.245e^-5	SYNONYMOUS_CODING Ir75a
X	5586604	X_5586604_SNP [dm3] X_5692571_SNP [dm6]	G	A	6.370e^-10	1.245e^-5	SYNONYMOUS_STOP cv DOWNSTREAM CG3149
3L	9412857	3L_9412857_DEL [dm3] 3L_9419757_DEL [dm6]	GATATGG	G	6.526e^-10	1.262e^-5	UPSTREAM CG3967 INTRON CG3967	TF binding site BDTNP1_TFBS_da mE1_TFBS_HSA
3R	15261513	3R_15261513_SNP [dm3] 3R_19435791_SNP [dm6]	A	G	6.762e^-10	1.271e^-5	INTRON CG31221
3R	5704329	3R_5704329_SNP [dm3] 3R_9878607_SNP [dm6]	T	C	6.843e^-10	1.271e^-5	UPSTREAM CR45029 INTRON Glut4EF	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
3R	25602933	3R_25602933_INS [dm3] 3R_29777211_INS [dm6]	A	AATGGCTAT	6.891e^-10	1.271e^-5	INTRON kay

Showing 1 to 100 of 1,000 entries

Previous1 2 3 4 5…10Next

By genomic position
Variant impact
Gene name

Censored phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results